Re: help with how pbc are defined.. .

From: Martin, Erik W (
Date: Fri Oct 12 2012 - 09:39:34 CDT

Thanks for the input. I'll add wrapNearest to the configurations file.
I'm aware that its cosmetic, but I frequently have to give presentations
to people not familiar with MD and I really prefer not answering questions
about unwrapped trajectoriesŠ

Maybe I wasn't entirely clear about the question though. What I wasn't
100% clear about was just how the boundary conditions are defined for
these non-cubic systems. I was hoping someone could either give me a
little information or point me to a good reference to read about this.

Thanks again,

On 10/11/12 1:34 PM, "David Hardy" <> wrote:

>For your NAMD configuration file, using "wrapNearest" with "wrapWater"
>should give your DCD trajectory the appearance of the octahedron without
>you having to do any additional wrapping of the positions. I don't know
>if the PBC wrapping in VMD has the option to apply a "wrapNearest" (i.e.,
>wrap to the image closest to the center) to an unwrapped trajectory. You
>probably already know that any kind of periodic wrapping is simply
>cosmetic and doesn't actually affect the simulation.
>On Oct 11, 2012, at 12:48 PM, Martin, Erik W wrote:
>> I've been using orthogonal boundary conditions for ages, and thought I
>>had a good handle on how this worked. However, I recently had to start
>>using a truncated octahedron and its become a bit of a mystery to me. I
>>followed what instructions I could find and defined my basis vectors as:
>> vector1 d 0 0
>> vector2 -1/3d 2/3sqrt(2) d 0
>> vector3 -1/3d -1/3sqrt(2)d -1/3sqrt(6)d
>> Or specifically in my case:
>> periodic cell dcdUnitCell yes cellBasisVector1 110.906 0.0 0.0
>>cellBasisVector2 -36.9688 104.5635 0.0 cellBasisVector3 -36.9688
>>-52.2818 -90.5547 cellOrigin 0.0 0.0 0.0
>> The first structure I started appears to be running just fine.
>>However, I left the line "wrapWater" out of the configuration file.
>>When I set up a second structure (all I changed was the water model to
>>tip4) I included this line. The simulation changed the structure to
>>some manner of parallelogram (see attached picture tip4_box1
>> Š The starting structure
>>is tip4_starting I
>>visualized the PBC with "pbc box" and saw that this was the shape of my
>>boundary conditions ­ albeit shifted. There appeared to be no error in
>>the running of the simulation, just this change. When I went back and
>>looked at the tip3 simulation, I found that the shape of the boundary
>>condition was the same, but seemed to have no impact on the structure
>>(picture tip3_box1:
>>However, when I used "pbc wrap" is forced everything into this boxŠ
>>oddly enough, when I attempted to "unwrap" the tip 4 simulation it
>>didn't return to the truncated octahedron.
>> Is there something I'm missing here about how the boundary conditions
>>are defined in the case of a truncated octahedron? Have I done
>>something wrong? Perhaps its simply not possible to use wrapWater with
>>this type of symmetry?
>> Thanks a lot for any help,
>> Erik
>> ________________________________
>> Email Disclaimer:
>> Consultation Disclaimer:
>David J. Hardy, Ph.D.
>Theoretical and Computational Biophysics
>Beckman Institute, University of Illinois

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